[ Identifiers | To Do | Deprecations ]

Identifier Index

[ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ ]

P

P1_SPACE_GROUP_SYMBOL (in schrodinger.application.matsci.nano.xtal)	PhpProject_getStep() (in _phase')	PrettyPubPreset (in schrodinger.application.bioluminate.pml_menus)
pack() (in schroPmwWrapper)	PhpProject_getTitle() (in _phase')	prev() (in _Step)
pack() (in GroundClass)	PhpProject_haveMasterDiffs() (in _phase')	prevent_overlapping_x_labels() (in schrodinger.application.bioluminate.sliderchart)
pack() (in schroWidget)	PhpProject_isValidArchiveName() (in _phase')	prevent_overlapping_x_labels() (in schrodinger.application.desmond.mplchart)
pack_stage() (in StageBase)	PhpProject_isValidProjectName() (in _phase')	preview() (in EditDialog)
Package (in schrodinger.application.licensing.flexlm)	PhpProject_logActivity() (in _phase')	PREVIOUS (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
PACKAGE_SUFFIX (in schrodinger.application.desmond.cmj)	PhpProject_needSyncFeatureDef() (in _phase')	previous (in SwigPyIterator)
packages (in schrodinger.application.combiglide)	PhpProject_newProject() (in _phase')	previous (in SwigPyIterator)
Packing (in schrodinger.protein._reliability)	PhpProject_openProject() (in _phase')	previous() (in SwigPyIterator)
PAGE_MARGIN (in PicturePrinter)	PhpProject_restoreMasterData() (in _phase')	previous() (in SwigPyIterator)
paint() (in _StructViewItem)	PhpProject_reviseDatabase() (in _phase')	previous() (in SwigPyIterator)
paint() (in _zoomViewItem)	PhpProject_sampleActives() (in _phase')	previous() (in SwigPyIterator)
paint() (in WorkspaceInclusionDelegate)	PhpProject_saveFeatureDef() (in _phase')	previous() (in SwigPyIterator)
paint_asl() (in Workspace)	PhpProject_saveFeatureFreq() (in _phase')	PRIMARY (in SpaceGroups)
paint_asl() (in schrodinger.application.desmond.maestro)	PhpProject_saveFeatureRadii() (in _phase')	PRIMARY_ALIGNMENT_DEFAULT (in schrodinger.application.matsci.nano.particle)
paint_mol() (in Workspace)	PhpProject_saveFeatureTol() (in _phase')	PRIMARY_ALIGNMENT_DEFAULT_LIST (in schrodinger.application.matsci.nano.particle)
paintCell() (in createFragmentDelegate)	PhpProject_saveFind() (in _phase')	PRIMARY_OPERATIONS_TAG (in SpaceGroup)
paintCell() (in simpleEnumDockDelegate)	PhpProject_saveMasterData() (in _phase')	PRIMARY_OPERS (in SpaceGroup)
PaintDeviceMetric	PhpProject_saveQsar() (in _phase')	prime (in schrodinger.application)
paintEvent() (in RowActionItem)	PhpProject_saveSiteMasks() (in _phase')	Prime (in schrodinger.application.prime.gui.analyze_energy)
paintEvent() (in WorkspaceInclusionCheckBox)	PhpProject_scaleActivity() (in _phase')	Prime (in schrodinger.application.prime.input)
paintEvent() (in DendrogramView)	PhpProject_setActivity() (in _phase')	prime (in schrodinger.application.vsw.stages)
paintEvent() (in sketcher)	PhpProject_setActivityMissing() (in _phase')	prime (in schrodinger.pipeline.stages)
paintEvent() (in sketcherGUIMultiColumnToolBar)	PhpProject_setGroup() (in _phase')	PRIME_ANTIB_LOOP_PRED (in Refiner)
paintEvent() (in sketcherView)	PhpProject_setMustMatch() (in _phase')	PRIME_ENTROPY (in _mmutil')
pair (in _FFIO)	PhpProject_setPharmSet() (in _phase')	PRIME_ENTROPY (in schrodinger.utils.mmutil)
pair_builtin_prop (in schrodinger.trajectory.ffstructure)	PhpProject_setQsarSet() (in _phase')	PRIME_LOOP_PRED (in Refiner)
PairDict (in schrodinger.application.desmond.energygroup)	PhpProject_setupFind() (in _phase')	PRIME_MINIMIZE (in Refiner)
pairmap (in _FEPIO)	PhpProject_setupQsar() (in _phase')	PRIME_RESIDUE (in Refiner)
PairMarker (in schrodinger.maestro.markers)	PhpProject_siteToStrings() (in _phase')	prime_search_and_scan() (in BondRotator)
PAIRS (in CheckInput)	PhpProject_swiginit() (in _phase')	PRIME_SIDECHAIN (in Refiner)
pairwise_align_ct() (in schrodinger.application.ska)	PhpProject_swigregister() (in _phase')	PRIME_SIDECHAIN_BB (in Refiner)
pairwise_align_pdb() (in schrodinger.application.ska)	PhpProject_syncFeatureDef() (in _phase')	PRIME_SIDECHAIN_CBETA (in Refiner)
paletteChange() (in DendrogramView)	PhpProject_testQsarModel() (in _phase')	prime_specs (in schrodinger.application.prime.input)
paletteChange() (in sketcher)	PhpProject_unzipArchive() (in _phase')	prime_workups (in schrodinger.test.stu.outcomes)
paletteChange() (in sketcherGUIMultiColumnToolBar)	PhpProject_unzipProject() (in _phase')	PrimeConfig (in schrodinger.application.bioluminate.protein)
paletteChange() (in sketcherView)	PhpProject_writeHypoFiles() (in _phase')	primefix (in schrodinger.application.prime)
paletteChanged() (in SimpleEnumDockPanel)	PhpProject_zipDirectory() (in _phase')	Primer (in schrodinger.application.desmond.stage)
paletteRefreshed() (in SimpleEnumDockPanel)	PhpProject_zipProject() (in _phase')	PrimeStage (in schrodinger.pipeline.stages.prime)
PanedWidget (in schrodinger.ui.widget.pmwwidget)	PhpSite (in schrodinger.infra.phase)	PrimeStructure (in schrodinger.application.bioluminate.protein)
PanedWindow (in schrodinger.ui.widget.tkinterwidget)	PhpSite___eq__() (in _phase')	primex_steric_clash_data_set (in Report)
panel() (in schrodinger.application.bioluminate.protein_report_widget)	PhpSite___ne__() (in _phase')	Primitive (in schrodinger.graphics3d.common)
panel() (in schrodinger.application.matsci.reordergui)	PhpSite_calculateSimilarity() (in _phase')	print_allow_adsorption_onto() (in schrodinger.application.matsci.rxn_channel.rxn_channel)
PanelModality	PhpSite_distance() (in _phase')	print_attachment_points() (in Data)
panels (in schrodinger.application.combiglide.combenumdock)	PhpSite_getProjectedOnly() (in _phase')	print_attachment_points_ct() (in Data)
Parallelepiped (in schrodinger.application.matsci.shapes)	PhpSite_getSiteNumber() (in _phase')	print_bad_jobs() (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
PARALLELEPIPED_SIDE_FACES (in schrodinger.application.matsci.nano.slab)	PhpSite_getSiteSimilarity() (in _phase')	print_debug() (in schrodinger.application.desmond.cmj)
PARAM (in schrodinger.application.desmond.cmj)	PhpSite_getSiteStatus() (in _phase')	print_deprecate() (in schrodinger.application.watermap.watermap_inp)
PARAM (in StageBase)	PhpSite_getSiteType() (in _phase')	print_fields() (in Feature)
PARAM (in Aacg_SiteMap_Multijob)	PhpSite_getSiteTypeChar() (in _phase')	print_fields() (in LicenseLine)
PARAM (in AlignCore)	PhpSite_getXCoord() (in _phase')	print_fields() (in Package)
PARAM (in Analysis)	PhpSite_getYCoord() (in _phase')	print_fields() (in Server)
PARAM (in AssignForcefield)	PhpSite_getZCoord() (in _phase')	print_fields() (in Vendor)
PARAM (in BuildGeometry)	PhpSite_setCoordinates() (in _phase')	print_help() (in Help)
PARAM (in CalcDdg)	PhpSite_setProjectedOnly() (in _phase')	print_help() (in Help)
PARAM (in CovalentFepMapper)	PhpSite_setProjectedOnlyOff() (in _phase')	print_if() (in schrodinger.application.desmond.util)
PARAM (in DesmondExtend)	PhpSite_setProjectedOnlyOn() (in _phase')	PRINT_INFO (in ParserWrapper)
PARAM (in Extern)	PhpSite_setSiteNumber() (in _phase')	print_job_info() (in schrodinger.application.macromodel.paraUtils)
PARAM (in FepAnalysis)	PhpSite_setSiteSimilarity() (in _phase')	print_last_lines_of_file() (in schrodinger.pipeline.stages.phase)
PARAM (in FepLauncher)	PhpSite_setSiteStatusOff() (in _phase')	print_pathway() (in schrodinger.application.desmond.fepana)
PARAM (in FepMapper)	PhpSite_setSiteStatusOn() (in _phase')	print_quiet() (in schrodinger.application.desmond.cmj)
PARAM (in FepMapperCleanup)	PhpSite_setSiteType() (in _phase')	print_report() (in schrodinger.application.canvas.driverutils)
PARAM (in FepMapperReport)	PhpSite_setSiteTypeChar() (in _phase')	print_silent() (in schrodinger.application.desmond.cmj)
PARAM (in FepMapping)	PhpSite_setStatus() (in _phase')	print_summary() (in schrodinger.test.stu.workup)
PARAM (in FepVrun)	PhpSite_setXCoord() (in _phase')	print_tonull() (in schrodinger.application.desmond.cmj)
PARAM (in ForcefieldBuilder)	PhpSite_setYCoord() (in _phase')	print_tree() (in Node)
PARAM (in LambdaHopping)	PhpSite_setZCoord() (in _phase')	print_usage() (in Startup)
PARAM (in MatSciAnalysis)	PhpSite_SiteStatusOff (in _phase')	print_usage() (in schrodinger.application.desmond.simulation_block_data)
PARAM (in McproSimulate)	PhpSite_SiteStatusOn (in _phase')	print_usage() (in schrodinger.application.desmond.simulation_block_test)
PARAM (in McproSystemBuilder)	PhpSite_swiginit() (in _phase')	print_usage() (in UI)
PARAM (in Minimize)	PhpSite_swigregister() (in _phase')	print_usage() (in SingleDashOptionParser)
PARAM (in Multisim)	PI (in schrodinger.application.matsci.shapes)	print_val() (in Test)
PARAM (in PLAnalysis)	PI_CAT_INTERACTION() (in sketcherStyle)	print_verbose() (in schrodinger.application.desmond.cmj)
PARAM (in ProteinFepMapper)	PI_PI_INTERACTION() (in sketcherStyle)	print_version() (in Help)
PARAM (in ProteinMutationGenerator)	PiCationInteraction (in schrodinger.infra.structure)	print_version() (in Startup)
PARAM (in ReplicaExchange)	PiCationParams (in schrodinger.infra.structure)	print_version() (in Help)
PARAM (in Simulate)	Pick3DObjectToggle (in schrodinger.ui.picking)	print_version() (in UI)
PARAM (in SolvatePocket)	PICK_ATOMS (in schrodinger.application.jaguar.gui.tabs.coordinates)	print_version() (in schrodinger.utils.cmdline)
PARAM (in SystemBuilder)	PICK_ATOMS_AND_BONDS (in schrodinger.application.jaguar.gui.tabs.coordinates)	print_Zmat() (in Zmat)
PARAM (in Task)	pick_by_atom() (in Rama)	printAction() (in Pipeline)
PARAM (in Trajectory)	pick_by_point() (in Rama)	printAction() (in StageJob)
PARAM (in Trim)	pick_category (in MaestroArrow)	printAllChannels() (in ChannelDefinitions)
PARAM (in Vrun)	pick_category (in MaestroSphere)	printAllSpgInfo() (in SpaceGroups)
PARAM (in WaterMap)	pick_id (in MaestroArrow)	printChannelDefs() (in Channels)
PARAM (in WaterMapCluster)	pick_id (in MaestroSphere)	printCrystalParams() (in Crystal)
PARAM (in WaterMapPostAnalysis)	PICK_MAX_ATOMS (in CoordinatePicker)	printDatabaseEntry() (in SpaceGroup)
param() (in Key)	PICK_TYPES (in schrodinger.application.jaguar.gui.tabs.coordinates)	printFailureMessage() (in StageJob)
param_in_parfile (in schrodinger.application.mcpro.writeinputs)	PickAtomToggle (in schrodinger.application.desmond.fep_gui)	printFiltered() (in Channels)
PARAMS (in Jcoupling)	PickAtomToggle (in schrodinger.ui.picking)	printFooter() (in TestUtility)
ParaStyle (in schrodinger.application.desmond.report_helper)	PickAtomToggle (in schrodinger.ui.widget.tkinterwidget)	printHeader() (in TestUtility)
paraUtils (in schrodinger.application.macromodel)	PickBondToggle (in schrodinger.application.desmond.fep_gui)	printHeader() (in TestQueue)
parent() (in Node)	PickBondToggle (in schrodinger.ui.picking)	printInfo() (in replica_container)
parent() (in Sea)	PickBondToggle (in schrodinger.ui.widget.tkinterwidget)	printInternals() (in InternalCoords)
parent_dir() (in schrodinger.application.desmond.util)	pickCompleted (in CoordinatePicker)	printJobParams() (in NanoSheets)
parent_structure() (in FFStructure)	pickCompleted() (in OptimizationTab)	printJobParams() (in NanoTubes)
pargph() (in schrodinger.application.desmond.report_helper)	pickCompleted() (in ScanTab)	printline() (in schrodinger.test.stu.outcomes.jaguar)
parse() (in TreeWizard)	picked() (in ColorChooserPanel)	printMultiWalledTubes() (in NanoTubes)
parse() (in TextParser)	picking (in schrodinger.ui)	printNotMinimized() (in Channels)
parse() (in Scan)	picking_atom_start() (in schrodinger.maestro.maestro)	printOnlyFailed() (in TestUtility)
parse() (in CriterionParser)	picking_bond_start() (in schrodinger.maestro.maestro)	printout() (in InputConfig)
parse() (in DefinitionParser)	picking_lasso_start() (in schrodinger.maestro.maestro)	printout() (in JobParameters)
parse() (in _MySplit)	picking_loss_notify() (in schrodinger.maestro.maestro)	printOverlapTable() (in schrodinger.trajectory.prody.compare)
parse_args() (in schrodinger.application.licensing.licadmin)	picking_stop() (in schrodinger.maestro.maestro)	printParameters() (in Minimizer)
parse_args() (in CmdlineParser)	Picklable (in schrodinger.application.desmond.picklejar)	printParams() (in GeneticOptimization)
parse_args() (in MopacAPI)	picklejar (in schrodinger.application.desmond)	printParams() (in Nanoparticle)
parse_args() (in HuntOptions)	PickleJar (in schrodinger.application.desmond.picklejar)	printParams() (in Surface)
parse_args() (in SingleDashOptionParser)	PickleState (in schrodinger.application.desmond.picklejar)	printProperties() (in GeneticOptimization)
parse_arguments() (in schrodinger.protein.getpdb_utility)	PickMixedToggle (in schrodinger.ui.picking)	printProps() (in MultiWalledNanoTube)
parse_basis() (in schrodinger.application.jaguar.basis)	pickProjTableAtom() (in MoleculeTabPka)	printProps() (in NanoTube)
parse_checkpoint_file() (in schrodinger.application.desmond.starter.generator.fep_plus)	pickThisAtom() (in MoleculeTabPka)	printRunSummary() (in TestUtility)
parse_command_line() (in schrodinger.application.vsw.vswinput)	PickToggle (in schrodinger.ui.widget.tkinterwidget)	printRxnReprs() (in Channels)
parse_components() (in schrodinger.application.licensing.flexlm)	PickTorsionToggle (in schrodinger.ui.picking)	printSingleWalledTubes() (in NanoTubes)
parse_date() (in schrodinger.application.licensing.flexlm)	PicturePrinter (in schrodinger.application.report2d)	printStatus() (in NewEntryGroup)
parse_eneseq() (in schrodinger.application.desmond.fepana)	PINFO (in _McproProt)	printStatus() (in JobDJ)
parse_expiration() (in schrodinger.application.licensing.flexlm)	PINK (in schrodinger.application.bioluminate.pml_menus)	printStatus() (in TestQueue)
parse_fep_data() (in FEPReportMaker)	PINK (in CoordinatePicker)	printSwapZmatAtom() (in ZmatAtom)
parse_file() (in Mopac2012TextParser)	PINK (in schrodinger.application.matsci.amorphous)	printSymmetryOpers() (in SpaceGroup)
parse_geometry() (in schrodinger.application.desmond.util)	pink (in Color)	printTestNumbers() (in TestUtility)
parse_indices() (in schrodinger.application.desmond.enhsamp)	pipeio (in schrodinger.pipeline)	printTree() (in DefinitionViewerDialog)
parse_it() (in schrodinger.application.desmond.title_to_hex)	PipeIO (in schrodinger.pipeline.pipeio)	printvals() (in schrodinger.infra.propedit)
parse_keyword_list() (in schrodinger.application.matsci.jobutils)	pipeline (in schrodinger)	printZmatAtom() (in ZmatAtom)
parse_lambda() (in schrodinger.application.desmond.config)	pipeline (in schrodinger.pipeline)	Priority
parse_lambda() (in schrodinger.application.desmond.gconfig)	Pipeline (in schrodinger.pipeline.pipeline)	priority() (in LicenseResource)
parse_line() (in schrodinger.application.licensing.flexlm)	pipeutils (in schrodinger.application.vsw)	PriorityQueue (in schrodinger.job.queue)
parse_lmdiag_entry() (in schrodinger.application.licensing.licadmin)	pipeutils (in schrodinger.pipeline)	PRISM (in schrodinger.application.matsci.shapes)
parse_lmdiag_output() (in schrodinger.application.licensing.licadmin)	PIPI_EDGE_TO_FACE_MAXIMUM_DISTANCE (in _structure')	PRO_COLOR (in Rama)
parse_lmgrd_event() (in schrodinger.application.licensing.licadmin)	PIPI_EDGE_TO_FACE_MAXIMUM_DISTANCE (in schrodinger.infra.structure)	prob (in schrodinger.application.desmond.ana)
parse_lmgrd_lines() (in schrodinger.application.licensing.licadmin)	PIPI_EDGE_TO_FACE_MINIMUM_ANGLE (in _structure')	probe_checkpoint() (in schrodinger.application.desmond.cmj)
parse_lmgrd_log() (in schrodinger.application.licensing.licadmin)	PIPI_EDGE_TO_FACE_MINIMUM_ANGLE (in schrodinger.infra.structure)	process_ark() (in _KeywordProcessor)
parse_lmhostid_output() (in schrodinger.application.licensing.licadmin)	PIPI_FACE_TO_FACE_MAXIMUM_ANGLE (in _structure')	process_attributes() (in schrodinger.application.licensing.licadmin)
parse_lmstat_output() (in schrodinger.application.licensing.licadmin)	PIPI_FACE_TO_FACE_MAXIMUM_ANGLE (in schrodinger.infra.structure)	process_bennett_log() (in replica_container)
parse_log_file() (in schrodinger.test.stu.outcomes.standard_workups)	PIPI_FACE_TO_FACE_MAXIMUM_DISTANCE (in _structure')	process_chunks() (in schrodinger.application.desmond.simulation_block_test)
parse_meta() (in schrodinger.application.desmond.meta)	PIPI_FACE_TO_FACE_MAXIMUM_DISTANCE (in schrodinger.infra.structure)	process_highlights() (in schrodinger.utils.pymol)
parse_mexpr() (in schrodinger.application.desmond.enhsamp)	PiPiInteraction (in schrodinger.infra.structure)	process_hypothesis() (in schrodinger.utils.pymol)
parse_msj() (in schrodinger.application.desmond.cmj)	PiPiParams (in schrodinger.infra.structure)	process_management (in schrodinger.test.stu)
parse_res_tag() (in schrodinger.application.desmond.fep_edge_report_maker)	PK_THRESH_DEF (in schrodinger.application.ligprep.ionizer)	process_measurements() (in schrodinger.utils.pymol)
parse_sba() (in schrodinger.application.desmond.simulation_block_data)	PKA_ATOM_PROP (in ProjEntryPka)	process_option_strings() (in SingleDashOption)
parse_sbt() (in schrodinger.application.desmond.simulation_block_test)	PKA_ATOM_PROP (in MoleculeTabPka)	process_pending_events() (in schrodinger.maestro.maestro)
parse_slice() (in schrodinger.application.desmond.util)	PKA_ATOM_ROLE (in schrodinger.application.jaguar.gui.input_tab_widgets_pka)	process_prj() (in schrodinger.utils.pymol)
parse_tokens() (in schrodinger.application.licensing.flexlm)	pl_image_tools (in schrodinger.application.desmond.event_analysis)	process_row() (in schrodinger.utils.pymol)
parseArgs() (in ParserWrapper)	PL_INTERACTIONS (in schrodinger.application.desmond.fep_edge_report_maker)	process_sequence() (in schrodinger.protein.helix)
parseArgs() (in ParserWrapper)	placeStructureInCell() (in AmorphousCellBuilder)	process_status() (in schrodinger.test.stu.process_management)
parseArgs() (in ParserWrapper)	PLAnalysis (in schrodinger.application.desmond.stage)	process_surface() (in schrodinger.utils.pymol)
parseArgs() (in ParserWrapper)	planar_groups (in schrodinger.protein.analysis_params)	processContextAction() (in ParticipantView)
parseArgs() (in ParserWrapper)	PlanarAngle (in schrodinger.trajectory.analysis)	processFrame() (in EnergyGroup)
parseArgs() (in ParserWrapper)	plane (in schrodinger.application.matsci.nano)	processFrame() (in MSEnergyGroup)
parseAtomText() (in StructureListWidget)	PLATFORM_WARNING (in schrodinger.application.desmond.gui)	processFrame() (in Angle)
parseCanvasCsv() (in Calculator)	PLATONIC (in schrodinger.application.matsci.shapes)	processFrame() (in AverageStructure)
parseConfigFile() (in schrodinger.test.stu.outcomes.jaguar)	plot (in schrodinger.application.desmond.mplchart)	processFrame() (in CenterOfMass)
ParseError (in schrodinger.application.desmond.cmj)	plot() (in Plotter)	processFrame() (in CenterOfMotion)
parseInput() (in Calculator)	plot() (in Reporter)	processFrame() (in CovarianceMatrix)
parseInputFile() (in MMKVSettings)	plot() (in Position)	processFrame() (in Dihedral)
parseLine() (in Criterion)	plot() (in Ramachandran)	processFrame() (in Distance)
parseNode() (in TreePatternParser)	plot() (in SecondaryStructure)	processFrame() (in HydrogenBondFinder)
parseOptions() (in CanvasFingerprintClusterCLI)	plot() (in AnalysisTool)	processFrame() (in HydrogenBondTracker)
parseOptions() (in CanvasFingerprintGeneratorCLI)	plot2D() (in AnalysisTool)	processFrame() (in LigandRMSD)
parseOptions() (in CanvasFingerprintSimilarityCLI)	plot_2d() (in Reporter)	processFrame() (in MolecularSurfaceArea)
parseOptions() (in _Main)	plot_lambda_window_overlap() (in schrodinger.application.desmond.fepana)	processFrame() (in PlanarAngle)
parsePropertyString() (in Property)	PLOT_TYPES (in ClusterStatisticsPlotDialog)	processFrame() (in PolarSurfaceArea)
Parser (in schrodinger.application.desmond.antlr3.recognizers)	PLOT_TYPES (in DistanceMatrixPlotDialog)	processFrame() (in Position)
parser (in schrodinger.application.desmond.cns_io)	PLOTALEA (in MopacResults71)	processFrame() (in RMSD)
parser (in schrodinger.application.desmond.system_builder_util)	PLOTALIE (in MopacResults71)	processFrame() (in RMSF)
parser (in schrodinger.application.licensing.licadmin)	PLOTESP (in MopacResults71)	processFrame() (in RadiusOfGyration)
parser (in schrodinger.application.watermap.watermap_inp)	Plotter (in schrodinger.analysis.enrichment)	processFrame() (in Ramachandran)
ParserMain (in schrodinger.application.desmond.antlr3.main)	plum (in Color)	processFrame() (in SecondaryStructure)
ParserRuleReturnScope (in schrodinger.application.desmond.antlr3.recognizers)	plus() (in Rama)	processFrame() (in SolventAccessibleSurfaceArea)
ParserWrapper (in schrodinger.application.matsci.nano.interface_mod)	PLUS_ICON (in schrodinger.application.matsci.msicons.controlicons)	processFrame() (in SolventAccessibleSurfaceAreaByResidue)
ParserWrapper (in schrodinger.application.matsci.nano.particle)	pml_menus (in schrodinger.application.bioluminate)	processFrame() (in VolumeMapper)
ParserWrapper (in schrodinger.application.matsci.nano.slab)	PML_PRESET_SURFACE (in schrodinger.application.bioluminate.pml_menus)	processFrame() (in AnalysisTool)
ParserWrapper (in schrodinger.application.matsci.nano.surfaces_interfaces_mod)	PML_SURFACE (in schrodinger.application.bioluminate.pml_menus)	processFrame() (in HydrophobicContactFinder)
ParserWrapper (in schrodinger.application.matsci.nano.xtal)	PMLContextMenu (in schrodinger.application.bioluminate.pml_menus)	processFrame() (in Jcoupling)
ParserWrapper (in schrodinger.application.matsci.rxn_path)	PMLMenu (in schrodinger.application.bioluminate.pml_menus)	processFrame() (in AreaPerLipid)
parseSolvent() (in DrawSolventPanel)	pmode() (in Sea)	processFrame() (in PhospholipidBilayerThickness)
parseStr() (in schrodinger.application.desmond.enhsamp)	Pmw_initialise() (in schrodinger.ui.widget.tkinterwidget)	processFrame() (in ProtLigInteractionFinder)
parseStream() (in LexerMain)	pmwwidget (in schrodinger.ui.widget)	processFrame() (in SaltBridgeFinder)
parseStream() (in ParserMain)	PNAME (in _McproProt)	processHbFrame() (in ProtLigInteractionFinder)
parseStream() (in WalkerMain)	PNAME0 (in _DesmondProt)	processHydrophobic() (in ProtLigInteractionFinder)
parseStream() (in _Main)	PNAME1 (in _DesmondProt)	processHydrophobicFrame() (in HydrophobicContactFinder)
parseTree() (in TreePatternParser)	PNAME2 (in _DesmondProt)	processJobOutputs() (in GeneratePropsStage)
parseWorkup() (in TestScript)	Point (in schrodinger.application.matsci.rxn_path)	processJobOutputs() (in LigFilterStage)
PART_FILL (in Partition)	point_group() (in schrodinger.application.jaguar.output)	processJobOutputs() (in DockingStage)
PARTIAL (in schrodinger.ui.widget.tkinterwidget)	POINT_GROUP_NAME (in SpaceGroup)	processJobOutputs() (in LigPrepStage)
partial_charge (in _StructureAtom)	POINT_GROUP_TAG (in SpaceGroup)	processJobOutputs() (in ConfSearchStage)
partial_charge (in ColorBy)	point_group_used() (in schrodinger.application.jaguar.output)	processJobOutputs() (in SampleRingsStage)
PARTIAL_CHARGE_4D (in schrodinger.application.bioluminate.pml_menus)	pointForIndex() (in Grid3D)	processJobOutputs() (in MMGBSAStage)
partial_structure_reader() (in schrodinger.test.stu.outcomes.prime_workups)	pointInside() (in ConvexPolyhedron)	processJobOutputs() (in PrimeStage)
participants() (in ReactionTab)	pointInside() (in Cylinder)	processJobOutputs() (in QikPropStage)
ParticipantView (in schrodinger.application.jaguar.gui.tabs.reaction_tab)	pointInside() (in Sphere)	processJobOutputs() (in QSiteStage)
particle (in schrodinger.application.matsci.nano)	pointIsOutOfBounds() (in Grid3D)	processJobOutputs() (in SemiEmpStage)
particle_position() (in _DesmondFrame)	POLAR_NOT_CHARGED_RESIDUES (in schrodinger.structutils)	processMetalFrame() (in ProtLigInteractionFinder)
particle_total() (in _DesmondFrame)	POLAR_POS (in StructuralInteractionFingerprintGenerator)	processOldDBs() (in ActiveDatabaseDialog)
particle_velocity() (in _DesmondFrame)	POLAR_RESIDUE (in StructuralInteractionFingerprintGenerator)	processPiCationFrame() (in HydrophobicContactFinder)
Partition (in schrodinger.application.combiglide.packages.hierarchy)	POLAR_RESIDUE() (in sketcherStyle)	processPiFrame() (in ProtLigInteractionFinder)
partitionAtoms() (in Nanoparticle)	POLAR_RESIDUES (in schrodinger.application.bioluminate.protein)	processPiPiFrame() (in HydrophobicContactFinder)
Partitioning (in schrodinger.application.combiglide.packages.hierarchy)	POLAR_RESIDUES (in schrodinger.structutils)	processProducts() (in Channels)
partitioning_names_at_levels (in CoreClassifier)	POLAR_RESIDUES (in StructuralInteractionFingerprintGenerator)	processSbFrame() (in ProtLigInteractionFinder)
PasswordRetryException (in schrodinger.utils.urllib)	PolarContactsObject (in schrodinger.application.bioluminate.pml_menus)	processWatersFrame() (in ProtLigInteractionFinder)
past_tense (in TestUtility)	PolarContactsOnlyMainchain (in schrodinger.application.bioluminate.pml_menus)	procText() (in schrodinger.application.desmond.enhsamp)
patch() (in _BaseClient)	PolarContactsOnlySidechain (in schrodinger.application.bioluminate.pml_menus)	PRODUCT (in ParserWrapper)
PATCH_ANALYZER (in _mmutil')	PolarContactsSubMenu (in schrodinger.application.bioluminate.pml_menus)	PRODUCT (in PerformanceTestCase)
PATCH_ANALYZER (in schrodinger.utils.mmutil)	PolarContactsToAnyAtoms (in schrodinger.application.bioluminate.pml_menus)	product (in schrodinger.test.stu.constants)
patch_count() (in Surface)	PolarContactsToAnyNonSolvent (in schrodinger.application.bioluminate.pml_menus)	product_dependencies (in schrodinger.test.stu.constants)
patch_vertices() (in Surface)	PolarContactsToEntry (in schrodinger.application.bioluminate.pml_menus)	PRODUCT_LIKE (in ParserWrapper)
PATH (in schrodinger.utils.env)	PolarContactsToEntryWithoutSolvent (in schrodinger.application.bioluminate.pml_menus)	PRODUCT_NAME_BASE (in Products)
path_geometry() (in schrodinger.application.jaguar.output)	PolarContactsWithoutIntraMainchain (in schrodinger.application.bioluminate.pml_menus)	PRODUCT_PREFIX (in schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab)
PATH_MAX (in _mmutil')	PolarContactsWithoutMainchain (in schrodinger.application.bioluminate.pml_menus)	PRODUCTPREFIX (in ReactionCoords)
PATH_MAX (in schrodinger.utils.mmutil)	PolarContactsWithoutSolvent (in schrodinger.application.bioluminate.pml_menus)	Products (in schrodinger.application.matsci.rxn_channel.rxn_channel)
PathModel (in schrodinger.application.desmond.fep_gui)	PolarContactsWithSidechains (in schrodinger.application.bioluminate.pml_menus)	prody (in schrodinger.trajectory)
pathModified() (in FileEntry)	PolarContactsWithSolvent (in schrodinger.application.bioluminate.pml_menus)	profile_get_current_parent() (in schrodinger.maestro.maestro)
pathname() (in Vendor)	POLARIZABILITY (in schrodinger.application.moldescriptors)	profiling (in schrodinger.job.hunt_stub)
pathname() (in LicenseResource)	PolarizabilitySubTab (in schrodinger.application.jaguar.gui.tabs.properties_tab)	profiling (in schrodinger.job.jobcontrol)
pathname() (in schrodinger.utils.sea)	PolarSurfaceArea (in schrodinger.trajectory.analysis)	PROG (in schrodinger.application.desmond.enhanced_sampling.mexpLexer)
PATTERN (in ChannelDefinition)	polygon (in schrodinger.graphics3d)	PROG (in schrodinger.application.desmond.enhanced_sampling.mexpParser)
pattern() (in TreePatternParser)	Polygon (in schrodinger.graphics3d.polygon)	prog() (in mexpParser)
PatternModel (in schrodinger.ui.ligfilter)	polyhedron (in schrodinger.graphics3d)	prog_return (in mexpParser)
PB_BOX_FACTOR (in schrodinger.application.desmond.fep_net_charge)	Polyhedron (in schrodinger.graphics3d.polyhedron)	PROJ_DIR (in ProjectTestCase)
PBC (in schrodinger.infra.structure)	POLYHEDRON_TYPES (in schrodinger.application.matsci.shapes)	project (in schrodinger)
PBC_BOND_COLOR (in PBCBond)	POLYMER (in schrodinger.application.bioluminate.pml_menus)	Project (in schrodinger.project)
PBC_BOND_COLOR_KEY (in PBCBond)	pop (in SwigDoubleVector)	PROJECT_CLOSE_CALLBACK (in schrodinger.maestro.maestro)
PBC_BOND_KEY (in PBCBond)	pop (in SwigDoubleVector3)	project_close_callback_add() (in schrodinger.maestro.maestro)
PBC_BOND_THRESHOLD (in PBCBond)	pop (in SwigIntVector)	project_close_callback_remove() (in schrodinger.maestro.maestro)
PBC_BONDING (in ParserWrapper)	pop (in SwigStringVector)	project_close_cancel() (in schrodinger.maestro.maestro)
pbc_manager (in schrodinger.trajectory)	pop (in SwigUInt64Vector)	project_get() (in schrodinger.maestro.maestro)
PBCBond (in schrodinger.application.matsci.nano.xtal)	pop (in SwigUnsignedIntVector)	PROJECT_HIERARCHICAL_GROUPING (in _mmutil')
PBCBonds (in schrodinger.application.matsci.nano.xtal)	pop (in SwigUnsignedIntVector2)	PROJECT_HIERARCHICAL_GROUPING (in schrodinger.utils.mmutil)
PBCMeasureMananger (in schrodinger.trajectory.pbc_manager)	pop (in SwigVectorIntIntPair)	PROJECT_RENAME_CALLBACK (in schrodinger.maestro.maestro)
pca (in schrodinger.trajectory.prody)	pop (in SwigDoubleVector)	project_rename_callback_add() (in schrodinger.maestro.maestro)
PCA (in schrodinger.trajectory.prody.pca)	pop (in SwigDoubleVector3)	project_rename_callback_remove() (in schrodinger.maestro.maestro)
PCLOSE (in schrodinger.application.desmond.enhanced_sampling.mexpLexer)	pop (in SwigIntVector)	project_table_get() (in schrodinger.maestro.maestro)
PCLOSE (in schrodinger.application.desmond.enhanced_sampling.mexpParser)	pop (in SwigStringVector)	project_table_synchronize() (in schrodinger.maestro.maestro)
PDB (in schrodinger.utils.fileutils)	pop (in SwigUInt64Vector)	project_table_update() (in schrodinger.maestro.maestro)
PDB_ATOM_NAME_KEY (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	pop (in SwigUnsignedIntVector)	PROJECT_UPDATE_CALLBACK (in schrodinger.maestro.maestro)
PDB_COMMON_NAMELEN (in _structure')	pop (in SwigUnsignedIntVector2)	project_update_callback_add() (in schrodinger.maestro.maestro)
PDB_COMMON_NAMELEN (in schrodinger.infra.structure)	pop (in SwigVectorIntIntPair)	project_update_callback_remove() (in schrodinger.maestro.maestro)
PDB_CRYSTAL_PROPS (in schrodinger.application.matsci.desmondutils)	pop() (in CommonTreeNodeStream)	projectClosed() (in ReactionTab)
PDB_R (in schrodinger.protein._reliability)	pop() (in PairDict)	projectClosedCallback() (in _App)
PDB_RES_NAME_KEY (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	pop() (in SwigDoubleVector)	ProjectException (in schrodinger.project)
PDB_RESOL (in schrodinger.protein._reliability)	pop() (in SwigDoubleVector3)	projectmodel (in schrodinger.infra)
PDB_RFREE (in schrodinger.protein._reliability)	pop() (in SwigIntVector)	ProjectRow (in schrodinger.project)
PDB_STRING (in SimplifiedSequenceViewer)	pop() (in SwigStringVector)	ProjectSurface (in schrodinger.surface)
pdbcode (in _StructureAtom)	pop() (in SwigUInt64Vector)	ProjectTableButton (in schrodinger.application.jaguar.gui.input_tab_widgets)
PdbMmpdbxAtom (in schrodinger.infra.structure)	pop() (in SwigUnsignedIntVector)	ProjectTestCase (in schrodinger.test.custom_test_classes)
pdbname (in _StructureAtom)	pop() (in SwigUnsignedIntVector2)	projectUpdated() (in InputTabMixin)
PDBNAME_ELEMENT_DICT (in schrodinger.application.prepwizard)	pop() (in SwigVectorIntIntPair)	projectUpdated() (in MultiStructureMixin)
PdbReader (in schrodinger.infra.structure)	pop() (in DoubleDoubleList)	projectUpdated() (in SubTabMixin)
PDBReader (in schrodinger.structure)	pop() (in DoubleList)	projectUpdated() (in InputEntriesModel)
pdbres (in _Residue)	pop() (in StringList)	projectUpdated() (in InputTabBase)
pdbres (in _StructureAtom)	pop() (in SwigAtomList)	projectUpdated() (in InputTabWithSubTabs)
pdbres() (in Ligand)	pop() (in SwigAtomPairList)	projectUpdated() (in MultiStructureTab)
PDBWriter (in schrodinger.structure)	pop() (in SwigAtomPairWithValueList)	ProjEntry (in schrodinger.application.jaguar.gui.input_tab_widgets)
PENALIZE (in schrodinger.application.glide.glide)	pop() (in SwigAtomQueryParamsList)	ProjEntryPka (in schrodinger.application.jaguar.gui.input_tab_widgets_pka)
PENALIZE_CHOICES (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	pop() (in SwigDcNonPbcAtomIdxList)	ProjEntryTuple (in schrodinger.application.jaguar.gui.input_tab_widgets)
PENALIZE_DEFAULT (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	pop() (in SwigDcPbcAtomList)	ProjEntryTuplePka (in schrodinger.application.jaguar.gui.input_tab_widgets_pka)
PENALIZE_PROTOCOLS (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	pop() (in SwigPiCationList)	PROJET_TABLE (in SimplifiedSequenceViewer)
PENALTYWEIGHT (in ParserWrapper)	pop() (in SwigPiPiInteractionList)	ProjTableLikeView (in schrodinger.application.jaguar.gui.utils)
PEOE_INTERVAL (in schrodinger.application.moldescriptors)	pop() (in SwigRingList)	promoteShowToolTip() (in InputEntriesProxyModel)
PEPTIDE_BOND_LENGTH_CUTOFF (in schrodinger.protein._reliability)	pop() (in SwigSaltBridgeList)	PromptDialog (in schrodinger.ui.widget.pmwwidget)
peptide_planarity_data_set (in Report)	pop() (in OneIndexedList)	PROP_BOOLEAN (in schrodinger.structure)
perAtomBasisChanged() (in InputEntriesModel)	pop() (in PriorityQueue)	PROP_CONVERSIONS (in schrodinger.application.bioluminate.protein)
perAtomBasisForEid() (in BasisSetModel)	pop() (in SwigDoubleVector)	PROP_FLOAT (in schrodinger.structure)
PerAtomBasisRow (in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets)	pop() (in SwigDoubleVector3)	PROP_INTEGER (in schrodinger.structure)
perAtomBasisSetsPresent() (in BasisSetSubTab)	pop() (in SwigIntVector)	PROP_LONG_NAME (in schrodinger.structure)
perAtomBasisSetsPresent() (in InputTabWithSubTabs)	pop() (in SwigStringVector)	prop_RE (in schrodinger.infra.propedit)
PERCENT (in schrodinger.application.desmond.antlr3.treewizard)	pop() (in SwigUInt64Vector)	PROP_REAL (in schrodinger.structure)
Percent_helix() (in schrodinger.utils.ligfilter)	pop() (in SwigUnsignedIntVector)	PROP_SHORT_NAME (in schrodinger.structure)
Percent_loop() (in schrodinger.utils.ligfilter)	pop() (in SwigUnsignedIntVector2)	PROP_STRING (in schrodinger.structure)
PERCENT_METAL_THRESHOLD (in schrodinger.application.matsci.nano.xtal)	pop() (in SwigVectorIntIntPair)	prop_type_names (in schrodinger.application.desmond.ffiostructure)
Percent_strand() (in schrodinger.utils.ligfilter)	pop() (in List)	prop_value (in Array_Prop)
percentage() (in _Rotamer)	pop_back (in SwigDoubleVector)	propedit (in schrodinger.infra)
perceptual_diff (in schrodinger.test.stu.outcomes.custom)	pop_back (in SwigDoubleVector3)	properties (in schrodinger.application.medchem.property)
perceptual_diff() (in schrodinger.test.stu.outcomes.custom.perceptual_diff)	pop_back (in SwigIntVector)	properties_do_not_exist() (in schrodinger.test.stu.outcomes.custom.glide)
perform_transmutations() (in schrodinger.application.matsci.enumeration)	pop_back (in SwigStringVector)	properties_tab (in schrodinger.application.jaguar.gui.tabs)
performance (in schrodinger.test)	pop_back (in SwigUInt64Vector)	properties_tab_ui (in schrodinger.application.jaguar.gui.ui)
performance_api_url() (in schrodinger.test.performance.reporter)	pop_back (in SwigUnsignedIntVector)	PropertiesMixin (in schrodinger.application.jaguar.gui.base_panel)
PerformanceTestCase (in schrodinger.test.performance.api)	pop_back (in SwigUnsignedIntVector2)	PropertiesTab (in schrodinger.application.jaguar.gui.tabs.properties_tab)
performSVD() (in PCA)	pop_back (in SwigVectorIntIntPair)	PropertiesTabBase (in schrodinger.application.jaguar.gui.tabs.properties_tab)
performTransmutation() (in Alchemist)	pop_back (in SwigDoubleVector)	PropertiesTabIGO (in schrodinger.application.jaguar.gui.tabs.properties_tab)
performTransmutation() (in ElementAlchemist)	pop_back (in SwigDoubleVector3)	PropertiesTableWidget (in schrodinger.application.jaguar.gui.utils)
performTransmutation() (in VacancyAlchemist)	pop_back (in SwigIntVector)	PropertiesValidatorMixin (in schrodinger.application.jaguar.gui.base_panel)
PERIODIC_CALLBACK (in schrodinger.maestro.maestro)	pop_back (in SwigStringVector)	property
periodic_callback_add() (in schrodinger.maestro.maestro)	pop_back (in SwigUInt64Vector)	property (in _Element)
periodic_callback_remove() (in schrodinger.maestro.maestro)	pop_back (in SwigUnsignedIntVector)	property (in _FEPIO)
PERL5LIB (in schrodinger.utils.env)	pop_back (in SwigUnsignedIntVector2)	property (in _FEPIOSubBlock)
PERL_FEATURE_FLAGS (in schrodinger.utils.mmutil)	pop_back (in SwigVectorIntIntPair)	property (in _FFIO)
PERMANENT_LICENSE_FAILURE (in JobStatus)	pop_back() (in SwigDoubleVector)	property (in _FFIOSubBlock)
persistentIndexList() (in RowModel)	pop_back() (in SwigDoubleVector3)	Property (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
PERSONAL_FRAGS_DIR (in schrodinger.application.combiglide.combenumdock)	pop_back() (in SwigIntVector)	property (in schrodinger.application.medchem)
PERSONAL_PALS_DIR (in schrodinger.application.combiglide.combenumdock)	pop_back() (in SwigStringVector)	property (in Structure)
PERT_NAME (in ModelSystem)	pop_back() (in SwigUInt64Vector)	property (in TextualStructure)
PertID (in schrodinger.application.mcpro.perturbations)	pop_back() (in SwigUnsignedIntVector)	property (in _StructureAtom)
PertReorder (in schrodinger.application.mcpro.perturbations)	pop_back() (in SwigUnsignedIntVector2)	property (in _StructureBond)
perturbation_databases (in schrodinger.application.mcpro.perturbations)	pop_back() (in SwigVectorIntIntPair)	property (in _FFAngle)
perturbations (in schrodinger.application.mcpro)	pop_back() (in DoubleDoubleList)	property (in _FFBond)
Perturbations (in schrodinger.application.mcpro.perturbations)	pop_back() (in DoubleList)	property (in _FFConstraint)
PFILE (in _McproProt)	pop_back() (in StringList)	property (in _FFDihedral)
PFILE0 (in _DesmondProt)	pop_back() (in SwigAtomList)	property (in _FFExclusion)
PFILE1 (in _DesmondProt)	pop_back() (in SwigAtomPairList)	property (in _FFPair)
PFILE2 (in _DesmondProt)	pop_back() (in SwigAtomPairWithValueList)	property (in _FFPseudo)
PH_DEF (in schrodinger.application.ligprep.ionizer)	pop_back() (in SwigAtomQueryParamsList)	property (in _FFRestraint)
PH_DIFF_TOL (in schrodinger.application.ligprep.ionizer)	pop_back() (in SwigDcNonPbcAtomIdxList)	property (in _FFSite)
PH_PRECISION (in schrodinger.application.ligprep.ionizer)	pop_back() (in SwigDcPbcAtomList)	property (in _FFVdwtype)
PH_THRESH_DEF (in schrodinger.application.ligprep.ionizer)	pop_back() (in SwigPiCationList)	property (in _FFVirtual)
phase (in schrodinger.application)	pop_back() (in SwigPiPiInteractionList)	PROPERTY (in schrodinger.utils.ligfilter)
phase (in schrodinger.application.vsw.stages)	pop_back() (in SwigRingList)	property_dict (in schrodinger.maestro.maestro)
phase (in schrodinger.infra)	pop_back() (in SwigSaltBridgeList)	property_is_consistent() (in schrodinger.test.stu.outcomes.custom.glide)
phase (in schrodinger.pipeline.stages)	pop_back() (in SwigDoubleVector)	PROPERTY_METHOD (in PolarizabilitySubTab)
PHASE (in schrodinger.utils.preferences)	pop_back() (in SwigDoubleVector3)	property_names (in schrodinger.application.matsci)
phase_markers (in schrodinger.application.phase)	pop_back() (in SwigIntVector)	PropertyCalculator (in schrodinger.application.bioluminate.protein)
PHASEDB (in schrodinger.application.vsw.vswinput)	pop_back() (in SwigStringVector)	PropertyCriterion (in schrodinger.utils.ligfilter)
PHASEDB (in schrodinger.pipeline.pipeio)	pop_back() (in SwigUInt64Vector)	PropertyDictionary (in schrodinger.project)
PhaseDB (in schrodinger.pipeline.pipeio)	pop_back() (in SwigUnsignedIntVector)	PropertyName (in schrodinger.structure)
PhaseFeatureMixin (in schrodinger.application.phase.phase_markers)	pop_back() (in SwigUnsignedIntVector2)	propertyselector (in schrodinger.ui)
PHI (in schrodinger.graphics3d.polyhedron)	pop_back() (in SwigVectorIntIntPair)	PropertySelector (in schrodinger.ui.propertyselector)
PhospholipidBilayerThickness (in schrodinger.trajectory.lipid_analysis)	pop_errors() (in ErrorHandler)	PropertySelectorMenu (in schrodinger.ui.propertyselector)
PhotoImage (in schrodinger.ui.widget.tkinterwidget)	pop_level() (in ErrorHandler)	PropertySelectorWithRanges (in schrodinger.application.bioluminate.propfilter)
PhpException (in schrodinger.infra.phase)	pop_level() (in schrodinger.infra.mmerr)	propfilter (in schrodinger.application.bioluminate)
PhpException_errCode_get() (in _phase')	POPEN (in schrodinger.application.desmond.enhanced_sampling.mexpLexer)	propfilter_ui (in schrodinger.application.bioluminate)
PhpException_errCode_set() (in _phase')	POPEN (in schrodinger.application.desmond.enhanced_sampling.mexpParser)	PropFilterDialog (in schrodinger.application.bioluminate.propfilter)
PhpException_errMesg_get() (in _phase')	Popen() (in schrodinger.utils.subprocess)	propka_parse (in schrodinger.application.bioluminate)
PhpException_errMesg_set() (in _phase')	popitem() (in PairDict)	propka_parse (in schrodinger.application.bioluminate.protein)
PhpException_swiginit() (in _phase')	populate_from_file() (in MopacResults2012)	PROPKA_SCRIPT (in schrodinger.application.bioluminate.run_propka)
PhpException_swigregister() (in _phase')	populateExcitedStatesType() (in ExcitedStateWidget)	PropkaError (in schrodinger.application.bioluminate.protein)
PhpException_what() (in _phase')	populatePickCombo() (in CoordinatePicker)	PROT_AND_DNA_SELE (in schrodinger.application.bioluminate.pml_menus)
PhpFeatureData (in schrodinger.infra.phase)	populateTypeCombo() (in CoordinatePicker)	PROT_FINAL_NAME (in ModelSystem)
PhpFeatureData_clear() (in _phase')	populateWeights() (in _ChargeSelectorPopUp)	PROT_NAME (in ModelSystem)
PhpFeatureData_exportToFile() (in _phase')	POPULATION (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	PROT_ONLY (in ModelSystem)
PhpFeatureData_exportToStream() (in _phase')	popUpUpdated() (in BasisSelectorLineEdit)	prot_toggle() (in _Flex)
PhpFeatureData_getDataColumn() (in _phase')	popUpUpdated() (in MutationSelectorComboBox)	protein (in schrodinger.application.bioluminate)
PhpFeatureData_getDataRow() (in _phase')	popUpUpdated() (in MutationSelectorLineEdit)	protein (in schrodinger)
PhpFeatureData_getDataValue() (in _phase')	port() (in Vendor)	PROTEIN_ASL (in schrodinger.application.matsci.nano.xtal)
PhpFeatureData_importFromFile() (in _phase')	pos() (in _fakeEvent)	PROTEIN_ASL (in schrodinger.trajectory.automatic_analysis_generator)
PhpFeatureData_importFromStream() (in _phase')	PoseLibrary (in schrodinger.application.glide.glideanalysis)	PROTEIN_ELEC_BLOCK (in schrodinger.application.desmond.fep_net_charge)
PhpFeatureData_numDataColumns() (in _phase')	poseviewconvert (in schrodinger.application.glide)	PROTEIN_MUTATION (in schrodinger.application.desmond.fep_gui)
PhpFeatureData_setDataRow() (in _phase')	posfbhw (in _FFIO)	PROTEIN_REPORT_LABEL (in schrodinger.protein._reliability)
PhpFeatureData_setDataValue() (in _phase')	Position (in schrodinger.trajectory.analysis)	protein_report_widget (in schrodinger.application.bioluminate)
PhpFeatureData_setDefaultDataRow() (in _phase')	position() (in _DesmondFrame)	protein_residue() (in FEPEdgeData)
PhpFeatureData_setDefaultDataValue() (in _phase')	POSITION_SCHEME (in schrodinger.application.bioluminate.pml_menus)	PROTEIN_RIP (in schrodinger.application.desmond.fep_net_charge)
PhpFeatureData_swiginit() (in _phase')	POSITIONAL (in schrodinger.application.glide.glide)	protein_sequences() (in SimplifiedSequenceViewer)
PhpFeatureData_swigregister() (in _phase')	PositionalConstraint (in schrodinger.application.glide.glide)	protein_structure_quality (in schrodinger.application.bioluminate)
PhpFeatureDefinition (in schrodinger.infra.phase)	POSITIVELY_CHARGED_RESIDUE() (in sketcherStyle)	protein_structure_quality_ui (in schrodinger.application.bioluminate)
PhpFeatureDefinition___eq__() (in _phase')	PosResDelegate (in schrodinger.application.desmond.gui)	ProteinCheckLabelSpinner (in schrodinger.application.desmond.feputils)
PhpFeatureDefinition___ne__() (in _phase')	PosResModel (in schrodinger.application.desmond.gui)	ProteinCheckParameters (in schrodinger.protein.reliability)
PhpFeatureDefinition_clear() (in _phase')	PosResRow (in schrodinger.application.desmond.gui)	ProteinCheckThread (in schrodinger.application.desmond.feputils)
PhpFeatureDefinition_getAllExcludes() (in _phase')	post() (in PMLContextMenu)	ProteinFepMapper (in schrodinger.application.desmond.stage)
PhpFeatureDefinition_getAllIncludes() (in _phase')	post() (in _BaseClient)	proteinHandler (in schrodinger.application.mcpro.zmat)
PhpFeatureDefinition_getExcludePattern() (in _phase')	post() (in _Cell)	ProteinMapperMsjGenerator (in schrodinger.application.desmond.mapper_msj_generator)
PhpFeatureDefinition_getExtendDistance() (in _phase')	post_system() (in schrodinger.test.performance.reporter)	ProteinMutationGenerator (in schrodinger.application.desmond.stage)
PhpFeatureDefinition_getFeatureComment() (in _phase')	postCommand() (in BaseJob)	ProteinReport (in schrodinger.application.desmond.replica_sid_generator)
PhpFeatureDefinition_getFeatureName() (in _phase')	PostLigPrepStage (in schrodinger.pipeline.stages.ligprep)	ProteinReportCheck (in schrodinger.test.structurecheck)
PhpFeatureDefinition_getFeatureNumber() (in _phase')	postProcess() (in AverageStructure)	ProteinStructureQualityViewer (in schrodinger.application.bioluminate.protein_structure_quality)
PhpFeatureDefinition_getFeatureType() (in _phase')	postProcess() (in CovarianceMatrix)	protliginteractionfinder (in schrodinger.trajectory)
PhpFeatureDefinition_getIncludePattern() (in _phase')	postProcess() (in AnalysisTool)	ProtLigInteractionFinder (in schrodinger.trajectory.protliginteractionfinder)
PhpFeatureDefinition_getNumExcludes() (in _phase')	poststage() (in StageBase)	PROTOCOL_VERSION (in DebugEventListener)
PhpFeatureDefinition_getNumIncludes() (in _phase')	poststage() (in FepAnalysis)	protonated_residues (in schrodinger.protein.analysis_params)
PhpFeatureDefinition_getProjectedType() (in _phase')	poststage() (in FepAnalysis2)	protonateResidue() (in ResidueTools)
PhpFeatureDefinition_getSasOptions() (in _phase')	poststage() (in FepMapperReport)	ProvidesBasisMixin (in schrodinger.application.jaguar.gui.tabs.base_tab)
PhpFeatureDefinition_setAllExcludes() (in _phase')	poststage() (in Stop)	ProvidesStructuresMetaclass (in schrodinger.application.jaguar.gui.tabs.base_tab)
PhpFeatureDefinition_setAllIncludes() (in _phase')	poststage() (in SystemBuilder)	ProvidesStructuresMixin (in schrodinger.application.jaguar.gui.tabs.base_tab)
PhpFeatureDefinition_setExcludePattern() (in _phase')	poststage() (in WaterMapCluster)	ProxyBasicAuthHandler (in schrodinger.utils.urllib)
PhpFeatureDefinition_setExtendDistance() (in _phase')	postTreatBuiltCell() (in AmorphousCellBuilder)	ProxyDigestAuthHandler (in schrodinger.utils.urllib)
PhpFeatureDefinition_setFeatureComment() (in _phase')	postTreatMinimizedStructure() (in ItemRow)	ProxyHandler (in schrodinger.utils.urllib)
PhpFeatureDefinition_setFeatureName() (in _phase')	postTreatMinimizedStructure() (in TMLigandRowMixin)	ProxyPasswordManager (in schrodinger.utils.urllib)
PhpFeatureDefinition_setFeatureNumber() (in _phase')	potential() (in BondRotator)	ProxyPasswordManagerQt (in schrodinger.protein.getpdb_utility)
PhpFeatureDefinition_setFeatureType() (in _phase')	PotentialEnergy (in schrodinger.application.desmond.simulation_block_test)	ProxyTunnelError (in schrodinger.utils.urllib)
PhpFeatureDefinition_setIncludePattern() (in _phase')	PotentialFrame (in schrodinger.ui.macromodel)	psd (in schrodinger.application.bioluminate.antibody.utils)
PhpFeatureDefinition_setProjectedTypeOff() (in _phase')	POWER_LAW_SCALING (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	Pseudo (in schrodinger.application.desmond.cms)
PhpFeatureDefinition_setProjectedTypeOn() (in _phase')	PR_NAME (in TimeSeriesAnalysisJob)	pseudo (in _FFIO)
PhpFeatureDefinition_setSasOptions() (in _phase')	PRECISION (in CanvasFingerprintGenerator)	pseudo_builtin_prop (in schrodinger.trajectory.ffstructure)
PhpFeatureDefinition_swiginit() (in _phase')	precision (in BondCharge)	pseudo_charge (in FFStructure)
PhpFeatureDefinition_swigregister() (in _phase')	precision (in Dipole)	pseudo_mass (in FFStructure)
PhpProject (in schrodinger.infra.phase)	precision (in FukuiIndices)	pseudo_position() (in _DesmondFrame)
PhpProject_addLigands() (in _phase')	precision (in Orbital)	pseudospectral() (in schrodinger.application.jaguar.output)
PhpProject_afterStep() (in _phase')	precision (in ThermoCollection)	PSP (in schrodinger.utils.preferences)
PhpProject_alignLigands() (in _phase')	precision (in ThermoProp)	psp_antibody (in schrodinger.application.bioluminate.antibody.management)
PhpProject_assignActives() (in _phase')	precision (in ZVariables)	psp_antibody (in schrodinger.application.bioluminate.antibody.utils)
PhpProject_assignDefaultGroups() (in _phase')	precision (in Scan)	psp_antibody (in schrodinger.application.bioluminate.pml_menus)
PhpProject_assignGroups() (in _phase')	PRECISION (in schrodinger.application.watermap.watermap_scoring)	PSP_PLOP (in _licensing')
PhpProject_assignInactives() (in _phase')	preCommand() (in BaseJob)	PSP_PLOP (in schrodinger.infra.licensing)
PhpProject_assignQsarSet() (in _phase')	preCommand() (in TestSPJob)	psp_search (in schrodinger.application.bioluminate.antibody.utils)
PhpProject_beforeStep() (in _phase')	PREDEFINED (in schrodinger.utils.ligfilter)	psp_util_import_err (in schrodinger.application.matsci.rxn_channel.rxn_channel)
PhpProject_buildQsarModel() (in _phase')	PREDEFINED_ATOM_GROUP (in schrodinger.application.desmond.mdkey)	pt_entry_id() (in ReactionParticipant)
PhpProject_closeProject() (in _phase')	predefined_function_dict (in schrodinger.utils.ligfilter)	PT_IMPORT_TXT (in ParticipantView)
PhpProject_combineFragmentCts() (in _phase')	PREDEFINED_GROUP_NAME (in _AtomGroup)	pull (in schrodinger.application.vsw.stages)
PhpProject_commitMasterData() (in _phase')	PREDEFINED_KEYS (in schrodinger.utils.ligfilter)	pull (in schrodinger.pipeline.stages)
PhpProject_compareFeatureDef() (in _phase')	PREDEFINED_STAGE_FAMILY (in schrodinger.application.desmond.stage)	pull_ligand() (in schrodinger.application.glide.http_server)
PhpProject_copyFile() (in _phase')	PredefinedCriterion (in schrodinger.utils.ligfilter)	pullCompounds() (in PullStage)
PhpProject_createSites() (in _phase')	predict() (in DFA)	pullHBonds() (in sketcherLID)
PhpProject_deleteHypotheses() (in _phase')	predict_correlation() (in schrodinger.application.desmond.correlation_tau)	pullPiInteractions() (in sketcherLID)
PhpProject_deleteLigands() (in _phase')	predict_kendall_tau() (in schrodinger.application.desmond.correlation_tau)	pullSaltBridges() (in sketcherLID)
PhpProject_deleteQsarModels() (in _phase')	predict_remd_temp (in schrodinger.application.desmond)	PullStage (in schrodinger.pipeline.stages.pull)
PhpProject_expActivity() (in _phase')	predict_temperature() (in schrodinger.application.desmond.predict_remd_temp)	purgeRecord() (in Job)
PhpProject_getAbsolutePath() (in _phase')	predict_temperature_ladder() (in schrodinger.application.desmond.remd)	push() (in CommonTreeNodeStream)
PhpProject_getActivity() (in _phase')	predict_with_nreplica_and_exch() (in schrodinger.application.desmond.remd)	push() (in Queue)
PhpProject_getActivityMissing() (in _phase')	predict_with_temp_and_exch() (in schrodinger.application.desmond.remd)	push() (in StageBase)
PhpProject_getBindingModes() (in _phase')	predict_with_temp_and_nreplica() (in schrodinger.application.desmond.remd)	push() (in PriorityQueue)
PhpProject_getConformer() (in _phase')	PREF_AB_SCHEME (in schrodinger.application.bioluminate.antibody.utils)	push_back (in SwigDoubleVector)
PhpProject_getConformerCount() (in _phase')	PREF_ACTIVE_DATABASES (in schrodinger.application.bioluminate.antibody.utils)	push_back (in SwigDoubleVector3)
PhpProject_getConformers() (in _phase')	PREF_ALL_DATABASES (in schrodinger.application.bioluminate.antibody.utils)	push_back (in SwigIntVector)
PhpProject_getDbID() (in _phase')	pref_dir (in schrodinger.application.bioluminate.pml_menus)	push_back (in SwigStringVector)
PhpProject_getDefaultFdFile() (in _phase')	PREF_GROUP (in schrodinger.application.matsci.builderwidgets)	push_back (in SwigUInt64Vector)
PhpProject_getDefaultFeatureFreq() (in _phase')	preferences (in schrodinger.application.bioluminate.antibody.utils)	push_back (in SwigUnsignedIntVector)
PhpProject_getDefaultFeatureRadii() (in _phase')	preferences (in schrodinger.utils)	push_back (in SwigUnsignedIntVector2)
PhpProject_getDefaultFeatureTol() (in _phase')	Preferences (in schrodinger.utils.preferences)	push_back (in SwigVectorIntIntPair)
PhpProject_getDefaultSiteMasks() (in _phase')	PREFIX_CALLOUTS (in schrodinger.utils.pymol)	push_back (in SwigDoubleVector)
PhpProject_getFdFile() (in _phase')	PREFIX_MAPS (in schrodinger.utils.pymol)	push_back (in SwigDoubleVector3)
PhpProject_getFeatureDef() (in _phase')	PREFIX_MEASUREMENTS (in schrodinger.utils.pymol)	push_back (in SwigIntVector)
PhpProject_getFeatureDefFromProj() (in _phase')	PREFIX_NAME (in _AtomGroup)	push_back (in SwigStringVector)
PhpProject_getFeatureFreq() (in _phase')	PREFIX_NAME_LEN (in _AtomGroup)	push_back (in SwigUInt64Vector)
PhpProject_getFeatureRadii() (in _phase')	PREFIX_SURFACES (in schrodinger.utils.pymol)	push_back (in SwigUnsignedIntVector)
PhpProject_getFeatureTol() (in _phase')	preflight() (in JaguarInput)	push_back (in SwigUnsignedIntVector2)
PhpProject_getGroup() (in _phase')	preoptimizeIsChecked() (in ReactionPropertiesTab)	push_back (in SwigVectorIntIntPair)
PhpProject_getGroupCount() (in _phase')	prep_struc() (in schrodinger.application.desmond.mdkey)	push_back() (in SwigDoubleVector)
PhpProject_getHypoAlignments() (in _phase')	prepActive() (in PrimeConfig)	push_back() (in SwigDoubleVector3)
PhpProject_getHypoIDs() (in _phase')	prepAntibodyLoop() (in PrimeConfig)	push_back() (in SwigIntVector)
PhpProject_getHypoMatches() (in _phase')	prepare() (in SysType)	push_back() (in SwigStringVector)
PhpProject_getHypoScores() (in _phase')	prepare() (in TyperBase)	push_back() (in SwigUInt64Vector)
PhpProject_getHypoSites() (in _phase')	prepare() (in WatermapTyper)	push_back() (in SwigUnsignedIntVector)
PhpProject_getHypoSitesStrings() (in _phase')	prepare() (in ReactionCoords)	push_back() (in SwigUnsignedIntVector2)
PhpProject_getInFileType() (in _phase')	prepare_command() (in RestInput)	push_back() (in SwigVectorIntIntPair)
PhpProject_getLigand() (in _phase')	prepare_for_epik() (in schrodinger.application.prepwizard)	push_back() (in DoubleDoubleList)
PhpProject_getLigandCount() (in _phase')	prepare_msj() (in RestInput)	push_back() (in DoubleList)
PhpProject_getLigandIDs() (in _phase')	prepare_next_generation_dirs_callback() (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	push_back() (in StringList)
PhpProject_getMatchedSites() (in _phase')	prepare_structure() (in RestInput)	push_back() (in SwigAtomList)
PhpProject_getMatchedSitesStrings() (in _phase')	prepareGeometryChange() (in DendrogramGraphicNode)	push_back() (in SwigAtomPairList)
PhpProject_getMolSites() (in _phase')	prepareGeometryChange() (in DendrogramGraphicNodeLabel)	push_back() (in SwigAtomPairWithValueList)
PhpProject_getMolSitesStrings() (in _phase')	prepareGeometryChange() (in DendrogramGraphicTree)	push_back() (in SwigAtomQueryParamsList)
PhpProject_getMustMatch() (in _phase')	prepareGeometryChange() (in sketcherAtom)	push_back() (in SwigDcNonPbcAtomIdxList)
PhpProject_getPharmSet() (in _phase')	prepareGeometryChange() (in sketcherBond)	push_back() (in SwigDcPbcAtomList)
PhpProject_getProjectPath() (in _phase')	prepareGeometryChange() (in sketcherGraphicalObject)	push_back() (in SwigPiCationList)
PhpProject_getQsarAlignments() (in _phase')	prepareGeometryChange() (in sketcherResidue)	push_back() (in SwigPiPiInteractionList)
PhpProject_getQsarCount() (in _phase')	prepareGeometryChange() (in sketcherResidueInteraction)	push_back() (in SwigRingList)
PhpProject_getQsarHypoIDs() (in _phase')	prepareInputLigands() (in SampleRingsStage)	push_back() (in SwigSaltBridgeList)
PhpProject_getQsarIDs() (in _phase')	prepareStructureForMinimization() (in ItemRow)	push_back() (in SwigDoubleVector)
PhpProject_getQsarModel() (in _phase')	prepareStructureForMinimization() (in TMLigandRowMixin)	push_back() (in SwigDoubleVector3)
PhpProject_getQsarModelClassDescription() (in _phase')	prepareStructures() (in WaterMapInput)	push_back() (in SwigIntVector)
PhpProject_getQsarModelClasses() (in _phase')	prepBldStruct() (in PrimeConfig)	push_back() (in SwigStringVector)
PhpProject_getQsarModelClassFraction() (in _phase')	prepend_mmfile_path() (in schrodinger.application.ligprep.ionizer)	push_back() (in SwigUInt64Vector)
PhpProject_getQsarModelCoeff() (in _phase')	prepend_path() (in schrodinger.utils.env)	push_back() (in SwigUnsignedIntVector)
PhpProject_getQsarModelCoeffRange() (in _phase')	prepEnergy() (in PrimeConfig)	push_back() (in SwigUnsignedIntVector2)
PhpProject_getQsarModelFactorCount() (in _phase')	prepLoop() (in PrimeConfig)	push_back() (in SwigVectorIntIntPair)
PhpProject_getQsarModelGridLimits() (in _phase')	prepMinimize() (in PrimeConfig)	push_level() (in ErrorHandler)
PhpProject_getQsarModelGridSpacing() (in _phase')	prepResidue() (in PrimeConfig)	push_level() (in schrodinger.infra.mmerr)
PhpProject_getQsarModelRegF() (in _phase')	preprocessMatchAtoms() (in NanoTube)	push_ligand() (in schrodinger.application.glide.http_server)
PhpProject_getQsarModelRegP() (in _phase')	prepSidechain() (in PrimeConfig)	put() (in _BaseClient)
PhpProject_getQsarModelRegRsqr() (in _phase')	prepSidechainBB() (in PrimeConfig)	putToM2ioFile() (in Structure)
PhpProject_getQsarModelRegRsqrCv() (in _phase')	prepSidechainCBeta() (in PrimeConfig)	putToM2ioFile() (in TextualStructure)
PhpProject_getQsarModelRegRsqrScramble() (in _phase')	prepwizard (in schrodinger.application)	PV (in schrodinger.application.glide.glide)
PhpProject_getQsarModelRegSD() (in _phase')	present_tense (in TestUtility)	pv2complex() (in schrodinger.application.glide.poseviewconvert)
PhpProject_getQsarModelRegStability() (in _phase')	PRESERVE_BONDING_KEY (in schrodinger.application.matsci.nano.xtal)	PV_SD (in schrodinger.application.glide.glide)
PhpProject_getQsarModelStyle() (in _phase')	PRESET_GCR (in schrodinger.application.bioluminate.protein_structure_quality)	PXerror (in schrodinger.application.prime.gui.analyze_energy)
PhpProject_getQsarModelVolBitCount() (in _phase')	PRESET_RT (in schrodinger.application.bioluminate.protein_structure_quality)	pxp_vdwr (in schrodinger.protein.analysis_params)
PhpProject_getQsarModelVolClasses() (in _phase')	PRESET_RYW (in schrodinger.application.bioluminate.protein_structure_quality)	pyepik (in schrodinger.application.epik)
PhpProject_getQsarModelVolCoords() (in _phase')	PresetAction (in schrodinger.application.bioluminate.pml_menus)	PYEVOLVE_LOG_EXT (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
PhpProject_getQsarModelVolOnBits() (in _phase')	PRESETS (in schrodinger.application.bioluminate.protein_structure_quality)	pylab (in schrodinger.analysis.enrichment)
PhpProject_getQsarProps() (in _phase')	PresetSubMenu (in schrodinger.application.bioluminate.pml_menus)	PYMOL (in schrodinger.utils.preferences)
PhpProject_getQsarSet() (in _phase')	Pressure (in schrodinger.application.desmond.simulation_block_test)	pymol (in schrodinger.utils)
PhpProject_getQsarStats() (in _phase')	pressure_tensor_pattern (in MSEnergyGroupAnalysis)	PYMOL_COLOR_CYCLE (in schrodinger.application.bioluminate.pml_menus)
PhpProject_getRuntimeName() (in _phase')	prestage() (in StageBase)	PYMOL_IONS (in schrodinger.application.bioluminate.pml_menus)
PhpProject_getSiteFragment() (in _phase')	prestage() (in FepMapperReport)	PymolInstance (in schrodinger.utils.pymol)
PhpProject_getSiteMasks() (in _phase')	prestage() (in Stop)	PymolScriptInstance (in schrodinger.utils.pymol)
PhpProject_getSitesConformer() (in _phase')	prestage() (in SystemBuilder)	PYTHON_MINIMIZE (in Refiner)
PhpProject_getSitesConformers() (in _phase')	PRESUMED_TS (in ParserWrapper)
PhpProject_getSlash() (in _phase')	PRESUMED_TS_CHOICES (in ParserWrapper)